Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula Gerardo D. L. Cervigni Æ Norma Paniego Æ Marina Dı ´az Æ Juan P. Selva Æ Diego Zappacosta Æ Darı ´o Zanazzi Æ In ˜ aki Landerreche Æ Luciano Martelotto Æ Silvina Felitti Æ Silvina Pessino Æ Germa ´n Spangenberg Æ Viviana Echenique Received: 15 February 2007 / Accepted: 22 December 2007 / Published online: 15 January 2008 Ó Springer Science+Business Media B.V. 2008 Abstract Eragrostis curvula (Schrad.) Nees is a forage grass native to the semiarid regions of Southern Africa, which reproduces mainly by pseudogamous diplosporous apomixis. A collection of ESTs was generated from four cDNA libraries, three of them obtained from panicles of near-iso- genic lines with different ploidy levels and reproductive modes, and one obtained from 12 days-old plant leaves. A total of 12,295 high-quality ESTs were clustered and assembled, rendering 8,864 unigenes, including 1,490 contigs and 7,394 singletons, with a genome coverage of 22%. A total of 7,029 (79.11%) unigenes were functionally categorized by BLASTX analysis against sequences deposited in public databases, but only 37.80% could be classified according to Gene Ontology. Sequence comparison against the cereals genes indexes (GI) revealed 50% significant hits. A total of 254 EST-SSRs were detected from 219 singletons and 35 from contigs. Di- and tri- motifs were similarly represented with percentages of 38.95 and 40.16%, respectively. In addition, 190 SNPs and Indels were detected in 18 contigs generated from 3 to 4 libraries. The ESTs and the molecular markers obtained in this study will provide valuable resources for a wide range of applications including gene identification, genetic mapping, cultivar identification, analysis of genetic diversity, phenotype mapping and marker assisted selection. Keywords cDNA libraries Á Eragrostis curvula Á ESTs Á Gene index Á Genic markers Abbreviations EST Expressed sequence tags 2,4-D 2,4 Dichlorophenoxyacetic acid BAP 6-Benzylamino purine DMSO Dimethyl sulfoxide IPTG Isopropyl-beta-D-thiogalactopyranoside D. Zanazzi Á I. Landerreche Bioaxioma, Venezuela 110-1P, Buenos Aires C1095AAD, Argentina D. Zanazzi Á I. Landerreche Facultad de Ingenierı ´a, Universidad de Buenos Aires, Av. Paseo Colo ´n 850, Buenos Aires C1063ACV, Argentina L. Martelotto Á S. Felitti Á S. Pessino Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Argentina G. Spangenberg Primary Industries Research Victoria, Plant Biotechnology Centre, La Trobe University, Bundoora, VIC 3086, Australia Gerardo D. L. Cervigni and Norma Paniego contributed equally to this manuscript. G. D. L. Cervigni Á M. Dı ´az Á J. P. Selva Á D. Zappacosta Á V. Echenique Centro de Recursos Naturales Renovables de la Zona Semia ´rida (CERZOS)–CONICET, Camino de La Carrindanga Km 7.0, Bahia Blanca 8000, Argentina N. Paniego Á V. Echenique Instituto de Biotecnologı ´a, CICVyA, INTA-Castelar, Buenos Aires, Argentina M. Dı ´az Departamento de Biologı ´a, Bioquı ´mica y Farmacia, Universidad Nacional del Sur, San Juan 670, Bahia Blanca 8000, Argentina J. P. Selva Á D. Zappacosta Á V. Echenique (&) Departamento de Agronomı ´a, Universidad Nacional del Sur, CERZOS–CONICET, San Andre ´s 800, Bahia Blanca 8000, Argentina e-mail: echeniq@criba.edu.ar 123 Plant Mol Biol (2008) 67:1–10 DOI 10.1007/s11103-007-9282-4